Ch 7 Exam 2 Flashcards
Mutations
changes in nucleotide sequence of DNA
spontaneous or induced
Spontaneous damage to DNA
Natural process in cells, DNA replication errors, or from reactive oxygen species from metabolism
Induced mutations
due to mutagen. Any chemical or physical agent that causes an increased in rate of mutations above the spontaneous background
Mutations can be good
widen the gene pool and offer genetic variations
rarely adventageous
Deleterious mutation
bad mutations, more common than advantageous mutation,
Point mutations
one substituation nucletodie
More trastic
expansion of trinucleotide repeats
insertion/deletions
major chromosomal rearrangements
transposable elements
are they random or are there places where they are more common
Hotspots for mutations
Transition mutations
replace one pyrimidine for another or a purine for antoher
transversion mutations
replace a pyrimidine w a purine or vice versa
Silent mutation
one base change but it doen’t change the amino acid sequence
missense mutation
one base change but amino avid changes
nonsense mutation
one base change and equals stop codon
example of missense mutation
sickle cell anemia
A to T transversion
Insertions and Deletions
-multiples of 3 in protein coding gene, either adds or sbutracts amino acids
-not a multple of 3 ends up changing the reading from
cystic fibriosis
deletion of one codon leading to one amino acid not being incoded
frame shift mutations
one base out changing the entire reading frame. everything after mutation changes the reading frame. taysacks disease. THyroid hormone RTH.
Whether or not a nucleotdie substitution hasve a phentypic effect depends on the
what type of mutation
do they alter a critical nucleotide in a gene regulatory region
do they alter a critical nucleotide in the template for the functional RNA molecule
Trinucleotide repeats lead to genetic instability
slip structures. Friedreich ataxia.
when two chromosomes pair up but don’t line up because there’s so much repeating can lead to
unequal crossing over
Types of mutations
deletion, duplication, inversion, nonreciprocal translocation, reciprocal translocation
Three classes of DNA damage from mutagens
single base changes, structural changes,
What are the three types of damage to DNA by mutagens and what is the first one
Single base change, strucural distortion, DNA backbone damage
Single base change: conversion affects the DNA sequence
only a minor effect on overall structure
Deamination - most frequent and important kind of hydrolytic damage. Removes an amine
Aklylation - adds an aklyl group
Oxidation - adds oxygen to the base
Deamination
an amino group is removed from a molecule. Single base changes
alkylation
single base changes. adds an alkyl group
Oxidation
single base changes. due to radiation sometimes. different base pairing capabilities
T-T dimers
when exposed to UV light two thymine fuse together. Blocks transcription and replication
DNA adducts
structurall distortions . One example is caused by an intercalating agent. The ethidium bromide changes the whole structure. 5-bromouracil is added instead of thymine leads to alterations.
DNA backbone damage
formation of abasic sites
-loss of nitrogenous base from nucleotide
Double stranded DNA breaks
Three cellular responses to DNA damage
Damage bypass
damage reversal
damage removal and replacement
Lesion bypass
allows for DNA replication to continue (TTdimers, hairpins, thins in the way)
Translesion synthesis (TLS)
Allows the damage to be bipassed
Some translesion repair mechanism are very accurate, most are error prone
Error prone DNA polymerase
may insert the incorrect nucleotide opposite lesion, may skp past and insert correct nucleotides opposite bases downstream (frameshift). Deaht, or high mutation rate? which would u prefer
DNA polymerase eta (n)
most accurate. translesion syntehsis past TT dimers by inserting AA.
Prokaryotes lesion bypass
DNA polymerases IV and V (not present under normal circomstanses)
Only when damage indicated by SOS response. Not actually repair, last ditch effort to live
Direct reversal of DNA damage
proteins recognize and fix.
DNA photolyase
DNA methyltransferase
SPRTN
DNA photolyase
reverses thymine dimers by using visual light. Uses energy to break TT dimers. 1
DNA methyltransferase
Takes methyl group off of incorrect base pair, fixing it
SPRTN protease
enzyme that takes off proteins that are stuck on the DNA. Controlled by ubiquitin.
When SPRTN protease is low
leads to cancer and disease
Removal repair
single base changes (base excision repair, mismatch repair)
Structural distortion (nucleotide excision repair)
what needs to be out of the way for repair to work
histones
How does base excision repair work
Histones leave, DNA glycosylase recognize and excise the damaged base, abasic site is either long or short pathway, scan the DNA looking for the specific base it can take out
short patch repair
B-lyase cuts the abasic strand of DNA on the 3’ end of the abasic site
APE1 removes the abasic phosphoribose
Pol B adds the new nucleotide
XRCC1/DNA ligase 3 seal the backboen
Long patch repair
APE1 cutes the abasic strand of DNA on 5’ end of the abasic site
Pol delta or epsilon displaces a short section of the ol strand and synthesizes new DNA
FEN1clips off the flap DNA
DNA ligase seals off the end
Repair pathways in general
- DNA glycosylase recognizes and excises the damaged base.
- an endonuclease cleaves the phosphodiester bond either 3’ or 5’ of the abasic site
- an endonuclease removes th1-10 nucleotides
- DNA polymerase replaces the missing nucleotides
- DNA ligase seals the gap
If there’s a mismatch?
Mut (mutator) proteins remove large sections of DNA
Proteins involved in mismatch repair
MSH, RPA, PCNA, MLH/PMS,
theme of DNA repair
hand off of damaged DNA from a complex with nuclease activity to a complex with polymerase activity to a complex with ligase activity
Nucleotide excision repair
Bigger change that needs to be fixed. Recognize lesion, take out about 30 nulceotides
Important proteins in nucleotide excision repair
XP (named after xeroderma pigmentosa)
then XPA etc RPA XPC (allow for recognition of the damage)
Exonucleases (cut out damage, 24-30 nucleotides).
two subtypes of excision repair
Global renome repair - identifies lesions in the whole genome
TRansition-coupled repair - identifies lesions in the transcibed sttrand of active genes
What’s the worst DNA damage that can happen to
Double-strand break, can lead to cell death
Double stranded DNA breaks repair mechanism
- homologous recombination repair
- Non-homologous end joining
Homologous recombination
Retrieves genetic information from an undamaged homologous chromosome
Nonhomologous end-joinnig
Direct ligation of DNA ends without any requirement for sequence homology
What proteins does homologous recombination repair
MRN and Rad 52 and BRCA
Heteroduplex DNA
duplex DNA formed during recombination composed of single DNA strands originally from different homologs. Comes from homologous recombination
Holliday Junction
recombination intermediate where 2 recombining duplexes are joined covalently by single-strand crossovers. Can be resolved in different ways (resolvasome).
Nonhomologous end-joining
Ku70 and 80 recognize damage, end processing and ligase getting it back together
Main proteins in non-homologous end joingin
Ku70 and Ku80
WHat happens if mutations are unrepaired
germ line mutations (gametes or in gamete precursor cells) transmitted to next gen
Somatic mutations (non-germ cells) not transmitted to next generation, can lead to cancer
